The Marburg virus has apparently run its course. Several months after the death of his wife and a nervous breakdown, Frank rejoins the FBI and investigates a plane crash with a new partner, Emma Hollis. But Frank finds it hard to work alongside the Millennium Group when he knows that they are responsible for the outbreak that claimed his wife's life.

Frank and Emma try to search for some answers when a gunmen fires upon high school students. Frank and Emma also learn that a survivalist group is responsible and they would even kill their own children, in order to ensure the survival of their computer corporation which is being threatened by the YK2 bug.